Genome sequence of Janthinobacterium sp. strain PAMC 25724, isolated from alpine glacier cryoconite.
ABSTRACT The draft genome of Janthinobacterium sp. strain PAMC 25724, which is a violacein-producing psychrotolerant bacterium, was determined. The strain was isolated from glacier cryoconite of the Alps mountain permafrost region. The sequence will allow identification and characterization of the genetic determination of its cold-adaptive properties.
- SourceAvailable from: Connie Lovejoy[Show abstract] [Hide abstract]
ABSTRACT: Extremely low abundance microorganisms (members of the "rare biosphere") are believed to include dormant taxa, which can sporadically become abundant following environmental triggers. Yet, microbial transitions from rare to abundant have seldom been captured in situ, and it is uncertain how widespread these transitions are. A bloom of a single ribotype (≥99% similarity in the 16S ribosomal RNA gene) of a widespread betaproteobacterium (Janthinobacterium sp.) occurred over 2 weeks in Arctic marine waters. The Janthinobacterium population was not detected microscopically in situ in January and early February, but suddenly appeared in the water column thereafter, eventually accounting for up to 20% of bacterial cells in mid February. During the bloom, this bacterium was detected at open water sites up to 50 km apart, being abundant down to more than 300 m. This event is one of the largest monospecific bacterial blooms reported in polar oceans. It is also remarkable because Betaproteobacteria are typically found only in low abundance in marine environments. In particular, Janthinobacterium were known from non-marine habitats and had previously been detected only in the rare biosphere of seawater samples, including the polar oceans. The Arctic Janthinobacterium formed mucilagenous monolayer aggregates after short (ca. 8 h) incubations, suggesting that biofilm formation may play a role in maintaining rare bacteria in pelagic marine environments. The spontaneous mass occurrence of this opportunistic rare taxon in polar waters during the energy-limited season extends current knowledge of how and when microbial transitions between rare and abundant occur in the ocean.Frontiers in microbiology. 01/2014; 5:425.
- [Show abstract] [Hide abstract]
ABSTRACT: Cryoconite holes are known as foci of microbial diversity and activity on polar glacier surfaces, but are virtually unexplored microbial habitats in alpine regions. In addition, whether cryoconite community structure reflects ecosystem functionality is poorly understood. Terminal-Restriction Fragment Length Polymorphism and Fourier Transform -Infra Red metabolite fingerprinting of cryoconite from glaciers in Austria, Greenland and Svalbard demonstrated cryoconite bacterial communities are closely correlated with cognate metabolite fingerprints. The influence of bacterial-associated fatty acids and polysaccharides was inferred, underlining the importance of bacterial community structure in the properties of cryoconite. Thus, combined application of T-RFLP and FT-IR metabolite fingerprinting promise high throughput and hence, rapid assessment of community structure-function relationships. Pyrosequencing revealed Proteobacteria were particularly abundant, with Cyanobacteria likely acting as ecosystem engineers in both alpine and Arctic cryoconite communities. However, despite these generalities, significant differences in bacterial community structures, compositions and metabolomes are found between alpine and Arctic cryoconite habitats, reflecting the impact of local and regional conditions on the challenges of thriving in glacial ecosystems. This article is protected by copyright. All rights reserved.FEMS Microbiology Ecology 01/2014; · 3.88 Impact Factor
- [Show abstract] [Hide abstract]
ABSTRACT: Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.Scientifica. 01/2013; 2013:512840.
Genome Sequence of Janthinobacterium sp. Strain PAMC 25724,
Isolated from Alpine Glacier Cryoconite
Su Jin Kim,aSeung Chul Shin,bSoon Gyu Hong,bYung Mi Lee,bHyoungseok Lee,bJungeun Lee,bIn-Geol Choi,aand Hyun Parkb
College of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul, South Korea,aand Korea Polar Research Institute, Yeonsu-gu, Incheon, South Koreab
Thedraftgenomeof Janthinobacterium sp.strainPAMC25724,whichisaviolacein-producingpsychrotolerantbacterium,was
monly isolated from the microbiota of soils and water of rivers,
soil (4, 7). Janthinobacterium sp. is one of the most common pur-
violacein (6), and it is suggested that the inhibitory effects of the
PAMC 25724 was isolated from glacier cryoconite of the Alps
mountain range, Austria (47°04=N, 12°41=E).
The genome of Janthinobacterium sp. PAMC 25724 was ana-
lyzed using a combined approach with the 454 GS FLX Titanium
system (Roche Diagnostics, Branford, CT) with an 8-kb paired-
end library (111,434 reads) and the Illumina GAIIx (San Diego,
GS FLX sequencing achieved about 8.7-fold coverage, while 208-
fold read coverage was achieved by Illumina paired-end sequenc-
ing. The reads generated by the Illumina GAIIx and the 454 GS
FLX Titanium were assembled using Celera assembler 6.1 (5).
(3), the rapid annotations using subsystems technology (RAST)
server (1), and the NCBI COG database (8). The draft genome se-
quence of Janthinobacterium sp. PAMC 25724 includes 4,985,247
5S rRNA genes, one 23S rRNA gene, and one 16S rRNA gene were
predicted in the draft genome. Approximately 84.9% of nucleotides
were predicted as protein-coding regions, and 73.7% (3,197) of the
Janthinobacterium sp. Marseille (score, 537), Herminiimonas arseni-
coxydans (score, 422), and Oxalobacter formigenes OXCC13 (score,
he genus Janthinobacterium includes violacein-producing,
Gram-negative, motile, rod-shaped bacteria that are com-
in this paper is the first version, AHHB01000000.
This work was supported by a Functional Genomics on Polar Organisms
grant (PE12020) funded by the Korea Polar Research Institute (KOPRI).
technology. BMC Genomics 9:75.
2. Brucker RM, et al. 2008. Amphibian chemical defense: antifungal metab-
Plethodon cinereus. J. Chem. Ecol. 34:1422–1429.
3. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improved
4. Johnson JH, Tymiak AA, Bolgar MS. 1990. Janthinocins A, B and C, novel
peptide lactone antibiotics produced by Janthinobacterium lividum. II.
Structure elucidation. J. Antibiot. (Tokyo) 43:920–930.
5. Myers EW, et al. 2000. A whole-genome assembly of Drosophila. Science
6. Pantanella F, et al. 2007. Violacein and biofilm production in Janthino-
bacterium lividum. J. Appl. Microbiol. 102:992–999.
8. Tatusov RL, et al. 2001. The COG database: new developments in phylo-
genetic classification of proteins from complete genomes. Nucleic Acids
Received 19 January 2012 Accepted 2 February 2012
Address correspondence to Hyun Park, firstname.lastname@example.org, or In-Geol Choi,
S.J.K. and S.C.S. contributed equally to this publication.
Copyright © 2012, American Society for Microbiology. All Rights Reserved.
jb.asm.org0021-9193/12/$12.00Journal of Bacteriologyp. 2096